22-31712753-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173566.3(PRR14L):c.5086A>G(p.Ile1696Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,551,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173566.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR14L | NM_173566.3 | c.5086A>G | p.Ile1696Val | missense_variant | 4/9 | ENST00000327423.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR14L | ENST00000327423.11 | c.5086A>G | p.Ile1696Val | missense_variant | 4/9 | 5 | NM_173566.3 | P1 | |
PRR14L | ENST00000431684.1 | c.1093A>G | p.Ile365Val | missense_variant, NMD_transcript_variant | 1/5 | 2 | |||
PRR14L | ENST00000330495.8 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000638 AC: 10AN: 156748Hom.: 0 AF XY: 0.0000845 AC XY: 7AN XY: 82870
GnomAD4 exome AF: 0.0000350 AC: 49AN: 1399536Hom.: 0 Cov.: 34 AF XY: 0.0000449 AC XY: 31AN XY: 690254
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.5086A>G (p.I1696V) alteration is located in exon 4 (coding exon 3) of the PRR14L gene. This alteration results from a A to G substitution at nucleotide position 5086, causing the isoleucine (I) at amino acid position 1696 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at